EXETER — The Environmental Protection Agency has issued a new water discharge permit to the town of Exeter that sets a strict cap on nitrogen discharge, beginning in 2013.

The EPA issued its final National Pollution Discharge Elimination System permit to Exeter on Wednesday. The permit sets a nitrogen discharge limit of 3 milligrams per liter for the community's wastewater treatment system.

Town officials in Exeter had hoped to avoid that limit. Exeter is one of five communities that have lodged a legal complaint against the state over the nitrogen discharge issue.

Exeter and other members of the Great Bay Municipal Coalition -- Dover, Rochester, Portsmouth and Newmarket -- argue the EPA and state environmental officials failed to use relevant science and ignored their feedback. The coalition agrees that nitrogen output should be reduced, but the communities are advocating for an 8 milligram per liter threshold.

In a statement issued Wednesday, the EPA said it has held months of discussions with officials in Exeter about the science and cost of necessary upgrades to meet the new environmental standard.

“EPA believes that the lengthy discussions have been worthwhile and have opened the door for an adaptive management approach that would allow Exeter to make phased improvements to their sewage treatment plant, which will help to control costs, and allow time for concurrent efforts by Exeter and others in the Squamscott River watershed to reduce other sources of nitrogen beyond the sewage treatment plant discharge,” reads the EPA's statement.

Newmarket became the first community to receive a final discharge permit earlier this year. Town officials announced Monday they had agreed to accept EPA's discharge regulations, despite their ongoing litigation over the issue.

Other communities around the Great Bay watershed are expecting to be next. Within the next two years, 12 more New Hampshire communities situated on waterways that link with Great Bay will receive a permit to limit the amount of nitrogen coming from sewage treatment plants.

“Nitrogen limits for each of the remaining sewage treatment plants will be developed on a case-by-case basis after consideration of the water quality impacts to associated receiving waters from individual discharges,” the EPA's statement reads.

The Squamscott River has high levels of nitrogen and low levels of dissolved oxygen due to sewage discharges and run-off. The dissolved inorganic nitrogen that comes from Exeter's sewage treatment plant is "believed to be responsible for much of the water quality impairment," according to the EPA.

The permit issued to Exeter on Wednesday includes a lengthy response to comments and concerns from the Great Bay Municipal Coalition about the science behind EPA's 3 milligram per liter nitrogen cap.

After reviewing the EPA's comments, Dover City Manager Michael Joyal said the EPA is once again indicating that it will not review the arguments submitted by the coalition because they were raised after a designated public comment period on the nitrogen standards expired.

“The EPA has opted to not respond to the legitimate science concerns presented by the Great Bay Municipal Coalition,” Joyal said in an email Wednesday.